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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Wed, Sep 30, 2020 at 9:17 PM <h_sahakyan.mb.sci.am> wrote: > > Hi Ray, > > Thank you for your reply > I used Amber18/AmberTools18. > > > The final system parameters are: > > NSTEP = 49990000 TIME(PS) = 111980.000 TEMP(K) = 309.04 PRESS = 0.0 > Etot = -264550.3893 EKtot = 68926.3047 EPtot = -333476.6940 > BOND = 2659.8247 ANGLE = 7371.0874 DIHED = 11181.7492 > 1-4 NB = 3195.8521 1-4 EEL = 32048.3876 VDWAALS = 36214.6452 > EELEC = -426148.2401 EHBOND = 0.0000 RESTRAINT = 0.0000 > EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1091009.1860 > Density = 1.0239 > > And here is the input file used for the production: > > prod > &cntrl > imin=0, > irest=1, > ntx=5, > nstlim=50000000, > dt=0.002, > ntc=2, > ntf=2, > tol=0.00001, > cut=10.0, > ntb=2, > ntp=1, > taup=2.0, > ntpr=10000, > ntwx=10000, > ntwr = 10000, > ntwe = 10000, > iwrap=1, > ntt=3, > barostat=2, > gamma_ln=2.0, > temp0=310.15, > tempi=310.15, > ig=-1, > / > > > Best regards, > Harutyun > > > > -------- Forwarded message ------- > From: "Ray Luo" <rluo.uci.edu> > To: "AMBER Mailing List" <amber.ambermd.org> > Sent: October 1, 2020 2:57 AM > Subject: Re: [AMBER] controversy in PBSA and GBSA results > Harutyun, > > Which version of Amber are you using? Also, it's better for us to see > your detailed energy output ... > > All the best, > Ray > -- > Ray Luo, Ph.D. > Professor of Structural Biology/Biochemistry/Biophysics, > Chemical and Materials Physics, Chemical and Biomolecular Engineering, > Biomedical Engineering, and Materials Science and Engineering > Department of Molecular Biology and Biochemistry > University of California, Irvine, CA 92697-3900 > > On Wed, Sep 30, 2020 at 4:44 AM <h_sahakyan.mb.sci.am> wrote: > > > Dear All, > > > > I used MM-PBSA/GBSA methods to calculate the binding free energy between two subunits of a protein. > > The binding energies were -101 and -94 kcal/mol for GBSA and PBSA respectively. However, in the > > presents of a ligand (between two subunits), binding energies were -124/-67 (GBSA/PBSA). As you can > > see, according to GBSA the ligand makes the interaction stronger and vice versa according to the > > PBSA calculation. What can be the reason for this controversy? > > > > I used MMPBSA.py with following input: > > > > pbsa_gbsa > > &general > > startframe=1, interval=50, endframe=5000, > > verbose=2, keep_files=0, netcdf=0, > > strip_mask = ":WAT,Cl-,Na+,K+,", > > ligand_mask = ":1-437,867,869", > > receptor_mask = ":438-865,866,868,870", > > / > > &gb > > saltcon=0.150, > > / > > &pb > > inp=1 # I tried inp=2 it gives more weird results, generally with positive energy values > > istrng=0.150 > > / > > Best wishes, > > Harutyun > > Senior Assistant at Laboratory of > > Computational Modeling of Biological Processes, > > Institute of Molecular Biology, NAS RA > > 7 Hasratyan St, Yerevan, Armenia > > Tel: +374 93 323990 > > E-mail: h_sahakyan.mb.sci.am (h_sahakyan.mb.sci.am) > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > -- > Senior Assistant at Laboratory of > Computational Modeling of Biological Processes, > Institute of Molecular Biology, NAS RA > 7 Hasratyan St, Yerevan, Armenia > Tel: +374 93 323990 > E-mail: h_sahakyan.mb.sci.am > > October 1, 2020 2:57 AM, "Ray Luo" <rluo.uci.edu> wrote: > > > Harutyun, > > > > Which version of Amber are you using? Also, it's better for us to see > > your detailed energy output ... > > > > All the best, > > Ray > > -- > > Ray Luo, Ph.D. > > Professor of Structural Biology/Biochemistry/Biophysics, > > Chemical and Materials Physics, Chemical and Biomolecular Engineering, > > Biomedical Engineering, and Materials Science and Engineering > > Department of Molecular Biology and Biochemistry > > University of California, Irvine, CA 92697-3900 > > > > On Wed, Sep 30, 2020 at 4:44 AM <h_sahakyan.mb.sci.am> wrote: > > > >> Dear All, > >> > >> I used MM-PBSA/GBSA methods to calculate the binding free energy between two subunits of a protein. > >> The binding energies were -101 and -94 kcal/mol for GBSA and PBSA respectively. However, in the > >> presents of a ligand (between two subunits), binding energies were -124/-67 (GBSA/PBSA). As you can > >> see, according to GBSA the ligand makes the interaction stronger and vice versa according to the > >> PBSA calculation. What can be the reason for this controversy? > >> > >> I used MMPBSA.py with following input: > >> > >> pbsa_gbsa > >> &general > >> startframe=1, interval=50, endframe=5000, > >> verbose=2, keep_files=0, netcdf=0, > >> strip_mask = ":WAT,Cl-,Na+,K+,", > >> ligand_mask = ":1-437,867,869", > >> receptor_mask = ":438-865,866,868,870", > >> / > >> &gb > >> saltcon=0.150, > >> / > >> &pb > >> inp=1 # I tried inp=2 it gives more weird results, generally with positive energy values > >> istrng=0.150 > >> / > >> Best wishes, > >> Harutyun > >> Senior Assistant at Laboratory of > >> Computational Modeling of Biological Processes, > >> Institute of Molecular Biology, NAS RA > >> 7 Hasratyan St, Yerevan, Armenia > >> Tel: +374 93 323990 > >> E-mail: h_sahakyan.mb.sci.am (h_sahakyan.mb.sci.am) > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Sep 30 2020 - 22:30:02 PDT